METHODS OF DETECTING miRNA

ABSTRACT

Described are non-invasive methods of detecting in vivo cell death by measuring levels of ubiquitous and tissue specific miRNA. The method can be applied for detection of pathologies caused or accompanied by cell death, as well as for diagnosis of infectious disease, cytotoxic effects induced by different chemical or physical factors, and the presence of specific fetal abnormalities.

RELATED APPLICATIONS

This application is a continuation of U.S. patent application Ser. No.12/293,378, filed Aug. 22, 2008, which claims the benefit of U.S.Provisional Application No. 60/965,871, filed on Aug. 22, 2007, thecontents of both applications are incorporated herein by reference intheir entireties as if fully set forth.

FIELD OF THE INVENTION

The invention provides non-invasive methods for isolation and detectionof cell-free small RNA, in particular microRNA (miRNA) sequences inbodily fluid. More specifically, the present invention encompassesmethods of detecting in vivo cell death by analyzing urine and otherbody fluids for miRNA levels for clinical diagnosis and treatmentmonitoring.

BACKGROUND OF THE INVENTION

Cell death is a normal component of development and functioning ofmulticellular organisms. Being a natural process, cell death is involvedin the pathology of numerous diseases caused by internal factors. Celldeath also accompanies diseases caused by external physical, chemical,of biological agents.

There exist two major types of cell death, necrosis and apoptosis,marked by different morphological and molecular characteristics (Kerr etal., Br. J. Cancer. 26, 239-257 (1972); Umansky, Theor. Biol. 97,591-602 (1982); Umansky et al., Adv Pharmacol. 41, 383-407 (1997);Ameisen Cell Death Differ. 11, 4-10 (2004); Lockshin et al. Int JBiochem Cell Biol. 36, 2405-19 (2004); G. Kroemer, et al., Cell Deathand Differentiation 12, 1463-1467 (2005)). Necrosis is considered to becatastrophic metabolic failure resulting directly from severe molecularand/or structural damage and leads to inflammation and secondary damageto surrounding cells. Apoptosis is a much more prevalent biologicalphenomenon than necrosis and can be induced by specific signals such ashormones, cytokines, by absence of specific signal such as growth oradhesion factors, or by molecular damage that does not causecatastrophic loss of integrity. Apoptosis is a result of an activecellular response involving initiation of an orderly and specificcascade of molecular events. Apoptosis leads to the appearance ofdistinctive chromatin condensation and margination, nuclearfragmentation, cell shrinkage, membrane blebbing and enzymaticinternucleosomal fragmentation of nuclear DNA (Umansky et al., BiochimBiophys Acta. 655, 9-17 (1981); Arends et al., Am J Pathol. 136, 593-608(1990)). Other more rare forms of cell death, characterized by specificmorphology, for example, so called autophagic cell death have also beendescribed (Bredesen et al., Stroke. 38(2 Suppl):652-660 (2007).

Independent of a specific mechanism and type of cell death, methods todetect dying cell types are important for diagnosis of various diseases,critical for disease and treatment monitoring, and helpful fordifferential diagnosis. Besides, the methods capable of detection ofspecific cell death in vivo are useful for developing drugs aiming atprevention or induction of cell death as well as for analysis of thecytotoxicity of the newly developed drugs.

There are some clinical tests for diagnosis of disease-related excessivecell death based on detection of tissue specific markers, such as forexample antigens, enzymes and other proteins in blood or in other bodilyfluids. Measurement of the activity of liver-specific enzymes in blood,for example, is a widely used method for evaluation of hepatocyte death(Amacher, et al., Regul Toxicol Pharmacol. April; 27(2):119-130 (1988);Salaspuro, et al., Enzyme. 37:87-107 (1987); Herlong, Hosp. Pract. (OffEd).29(11):32-38 (1994)). Evaluation of the level of cardiomyocytespecific antigens has also been used for diagnosis of the myocardialinfarction (Mair et al., Clin Chem Lab Med. 37:1077-1084 (1999); Nuneset al., Rev Port Cardiol. 20:785-788 (2001)). However, the number ofsuch techniques is limited to diseases in which a marker and a method ofdetection are known in order for the analysis to provide meaningful,tissue-specific results (Oh S et al., Curr Gastroenterol Rep. 3:12-18(2001); Rochling et al., Clin Cornerstone. 3(6):1-12 (2001)). Othermethods require invasive biopsy of specific tissues suspected of havinga diseased condition to get a specimen for analysis. However, biopsy ofsome organs and tissues, for example brain is highly invasive and oftendifficult to perform.

It is well known that apoptosis, or programmed cell death, which is amajor form of cell death in the mammalian organism, is accompanied byinternucleosomal fragmentation of nuclear DNA. Many laboratories havedemonstrated that a portion of this DNA appears in blood (Lo Y. M. AnnNY Acad Sci. 945:1-7 (2001); Lichtenstein et al., Ann NY Acad Sci.945:239-249 (2001); Taback et al., Curr Opin Mol Ther. 6:273-278 (2004);Bischoff et al., Hum Reprod Update. 8:493-500, (2002)). It has also beenshown that this fragmented DNA, called transrenal DNA (Tr-DNA) crossesthe kidney barrier and can be detected in the urine (Botezatu et al.,Clin Chem. 46:1078-1084, (2000); Su et al., J Mol Diagn. 6:101-107(2004); Su et al., Ann NY Acad Sci. 1022:81-89 (2004).

Although both cell-free plasma DNA and Tr-DNA may be used as diagnostictools, they provide a rather limited approach when evaluating tissuespecific events, such as cell death. Thus analytical methods that arenon-invasive, and provide a broader range of indications of specificpathology, due to their ability to detect levels of dying cells inparticular tissues and organs, would be useful for diagnosing andmonitoring the state of various diseases or pathological conditions inpatients. In addition, tissue specific analytical methods that providethe means for monitoring the response of a patient to a disease therapywould be useful to determine the therapy effectiveness, and in the caseof drug treatment, the optimum dosage required for drug administration.

To address these problems, the instant invention is focused on the useof micro RNA (miRNA) as a diagnostic tool to monitor in vivo cell deathin bodily fluids, such as for example serum and urine. Unlike cell-freeplasma DNA and Tr-DNA, many miRNAs exhibit cell, tissue and organspecific expression profiles (Liang et al., Genomics, 8:166 (2007);Lukiw et al, Neuroreport. 18:297-300 (2007); Lagos-Quintana et al., CurrBiol. 12:735-739 (2002); Chen et al., Nat Genet. 38:228-233 (2006);Beuvink et al., J. Nucleic Acids Res. 35:e52 (2007)). Furthermore,correlation of miRNA cell and tissue specific profiles with differentpathologies and tumor types have been demonstrated (Visone R., et al.Oncogene. 26:7590-7595 (2007); Nelson et al., Neuropathol Exp Neurol.66:461-468 (2007); Negrini et al., J Cell Sci. 120:1833-1840 (2007);Chang et al., Annu Rev Genomics Hum Genet. 8:215-239 (2007); Jay et al.,Cell Biol. 26:293-300 (2007)).

Thus, the instant invention provides methods for measuring in vivo celldeath by detection of tissue-specific miRNAs, characteristic of aspecific pathology, in body fluids, such as for example serum and urine.The instant methods based on detection of miRNAs in bodily fluids areused for further development of diagnostic or monitoring tests.

SUMMARY OF THE INVENTION

The instant invention relates to a novel method for detecting andmeasuring in vivo cell-death by analyzing levels of specific miRNAsequences in cell-free nucleic acids obtained from bodily fluids, saidmiRNA originating from cells dying throughout the body, and using theobtained analytical result to determine state of a disease or abnormalmedical condition in a patient.

The methods of the instant invention are based on adsorption ofcell-free nucleic acids on and elution from anion-exchangers, whichmakes it possible to concentrate and isolate nucleic acid fragmentslarger then 10 nucleotides. Specifically, the instant inventiondemonstrates: (i) the presence of miRNA in body fluids; (ii) detectionin urine of miRNA that originated from organs located outside of urinarysystem, which means that they have crossed the kidney barrier, such asfor example, transrenal miRNA (Tr-miRNA); iii) detection of miRNA inserum (iv) pathology associated with cell death in a particular cell,tissue and/or organ is accompanied by changes in levels of miRNAspecific for the said organ.

The present invention provides a method of detecting and quantitatingcell, tissue and/or organ-specific cell-free miRNAs in body fluid forevaluation of in vivo cell death in various tissue and organs, whereinin vivo cell death is associated with a disorder of a particular tissueand/or organ comprising obtaining a body fluid sample from a subject;and analyzing said body fluid sample for one or more specific sequencesof miRNA, wherein said analyzing comprises the step of detecting saidmiRNA with a primer and/or probe that is substantially complementary toa part of said specific miRNA sequences. In some embodiments of thepresent invention, excessive or insufficient in vivo cell death isassociated with a disorder of particular tissue.

In one embodiment of the present invention, the body fluid is urine. Inanother embodiment, the present method of analysis of a urine sampleincludes a technique selected from the group consisting ofhybridization, cycling probe reaction, polymerase chain reaction, nestedpolymerase chain reaction, PCR to analyze single strand conformationpolymorphisms and ligase chain reaction. In yet another embodiment,nucleic acid degradation in said urine sample is reduced.

The method of the present invention includes reducing nucleic aciddegradation comprising inhibiting nuclease activity by addition of RNAseinhibitor(s), heat inactivation, or by treating said urine sample with acompound selected from the group consisting of: guanidine-HCl, guanidineisothiocyanate, N-lauroylsarcosine, and sodium dodecylsulphate. In oneembodiment of the present invention, urine sample has been held in thebladder less than 12 hours.

In one embodiment of the present invention, the body fluid is serum. Themethod of the present invention includes analysis of a serum sampleincluding a technique selected from the group consisting ofhybridization, cycling probe reaction, polymerase chain reaction, nestedpolymerase chain reaction, PCR to analyze single strand conformationpolymorphisms and ligase chain reaction.

In yet another embodiment, the method of the instant invention involvesdetecting cell-free miRNAs, as a specific marker for the specificdisorder associated with excessive or insufficient cell death in atissue or organ. Optionally, said disorder is a pathogen infection.Preferably, said pathogen is a virus. More preferably, said virus is anEpstein-Barr virus. Optionally, said disorder is a brain stroke,Alzheimer's disease, Parkinson's disease, associated with pregnancyand/or fetus or Down syndrome.

The present invention provides a method of detecting in urine cell-freemiRNAs, originating in different organs and tissues, including areasother than urinary system, in a subject as a result of disorderassociated with excessive or insufficient cell death in a tissue ororgan, comprising obtaining a urine sample from a subject; and analyzingsaid urine sample for one or more specific sequences of miRNA whereinsaid analyzing comprises the step of detecting said miRNA with a primerand/or probe that is substantially complementary to a part of saidspecific miRNA sequences.

The method of the present invention provides a method of disease and/ortreatment monitoring in a subject by quantitative analysis of specificcell-free miRNAs in a body fluid, comprising periodically obtaining abody fluid sample from a subject; and analyzing said sample for one ormore specific sequences of miRNA that are specific/over-expressed incells, tissue or organ of interest, wherein said analyzing comprises thestep of detecting said miRNA with primers and/or probe that issubstantially complementary to a part of said specific miRNA sequences.In one embodiment, the body fluid is urine. In another embodiment, thebody fluid is serum.

BRIEF DESCRIPTION OF THE DRAWINGS

The foregoing and other objects, features, and advantages of theinvention will be apparent from the more particular description ofembodiments of the invention, as illustrated in the accompanyingdrawings. The drawings are not necessary to scale, emphasis insteadbeing placed upon illustrating the principles of the invention.

FIG. 1 is a photograph of a polyacrylamide gel electrophoresis ofnucleic acids extracted from filtered urine using Q-Sepharose™.

FIG. 2 is a photograph of a polyacrylamide gel analysis of EBV derivedBART1 miRNA specific RT-PCR product.

FIGS. 3A to 3G are dot plot representations of the normalizedconcentrations of miRNA in urine samples of patients at 12 and 24 hourtime points after brain stroke.

FIG. 4 is a diagram representing correlation between changes in miRNAs129 and 219 concentrations and brain stroke outcome. The patientslabeled as ∘ and □ improved their clinical status a month after stroke,and the clinical status of the patient labeled x has deteriorated amonth after a stroke.

FIG. 5 is a dot plot representation of the normalized concentrations ofmiRNA in unfiltered urine samples of patients with Alzheimer's diseaseand age matched controls.

FIG. 6 is a dot plot representation of the normalized concentrations ofmiRNA in filtered urine samples of patients with Alzheimer's disease andage matched controls.

FIG. 7 is a dot plot representation of the normalized concentrations ofmiRNA in serum samples of patients with Alzheimer's disease and agematched controls.

FIG. 8 is a dot plot representation of the normalized concentrations ofmiRNA in urine samples of patients with Parkinson's disease and agematched controls.

FIG. 9 is a dot plot representation of the normalized concentration ofmiRNA-9 in urine samples of women pregnant with Down syndrome and normalfetuses.

DETAILED DESCRIPTION OF THE INVENTION

The technology of this invention is based on the discovery that smallRNAs, in particular specific micro RNAs (miRNAs), including transrenalmiRNA (Tr-miRNA), are presented in bodily fluids and theirconcentrations reflect cell death associated with organ damage or otherpathology. The presence of these nucleic acid sequences at levels loweror higher than that of a control group is therefore an indication thatan abnormality or pathological condition is likely present in thepatient from whom the sample was obtained.

The methods of the present invention offer improvements over previousmethods of diagnosis, detection and monitoring due to their inherentlynon-invasive nature.

To facilitate the understanding of the invention, a number of terms aredefined below:

The term “primer” refers to an oligonucleotide which is capable ofacting as a point of initiation of synthesis when placed underconditions in which primer extension is initiated. An oligonucleotide“primer” can occur naturally, as in a purified restriction digest or beproduced synthetically.

A primer is selected to be “substantially” complementary to a strand ofspecific sequence of the template. A primer must be sufficientlycomplementary to hybridize with a template strand for primer elongationto occur. A primer sequence need not reflect the exact sequence of thetemplate. For example, a non-complementary nucleotide fragment may beattached to the 5′ end of the primer, with the remainder of the primersequence being substantially complementary to the strand.Non-complementary bases or longer sequences can be interspersed into theprimer, provided that the primer sequence has sufficient complementaritywith the sequence of the template to hybridize and thereby form atemplate primer complex for synthesis of the extension product of theprimer.

A “target” nucleic acid is a miRNA sequence to be evaluated byhybridization, amplification or any other means of analyzing a nucleicacid sequence, including a combination of analysis methods.

“Hybridization” methods involve the annealing of a complementarysequence to the target nucleic acid (the sequence to be analyzed). Theability of two polymers of nucleic acid containing complementarysequences to find each other and anneal through base pairing interactionis a well-recognized phenomenon. The initial observations of the“hybridization” process by Marmur and Lane, Proc. Natl. Acad. Sci. USA46:453 (1960) and Doty et al., Proc. Natl. Acad. Sci. USA 46:461 (1960)have been followed by the refinement of this process into an essentialtool of modern biology. Hybridization encompasses, but not be limitedto, slot, dot and blot hybridization techniques.

It is important for some diagnostic applications to determine whetherthe hybridization represents complete or partial complementarity. Forexample, where it is desired to detect simply the presence or absence ofpathogen miRNA, it is only important that the hybridization methodensures hybridization when the relevant sequence is present; conditionscan be selected where both partially complementary probes and completelycomplementary probes will hybridize. Other diagnostic applications,however, may require that the hybridization method distinguish betweenpartial and complete complementarity. It may be of interest to detectgenetic polymorphisms.

The term “probe” as used herein refers to an oligonucleotide (i.e., asequence of nucleotides), whether occurring naturally as in a purifiedrestriction digest or produced synthetically, which forms a duplexstructure or other complex with a sequence of another nucleic acid, dueto complementarity or other means of reproducible attractiveinteraction, of at least one sequence in the probe with a sequence inthe other nucleic acid. Probes are useful in the detection,identification and isolation of particular gene sequences. It iscontemplated that any probe used in the present invention will belabeled with any “reporter molecule,” so that it is detectable in anydetection system, including, but not limited to, enzyme (e.g., ELISA, aswell as enzyme-based histochemical assays), fluorescent, radioactive,and luminescent systems. It is further contemplated that theoligonucleotide of interest (i.e., to be detected) will be labeled witha reporter molecule. It is also contemplated that both the probe andoligonucleotide of interest will be labeled. It is not intended that thepresent invention be limited to any particular detection system orlabel.

As used herein, the term “miRNA” is a subclass of small non-codingsingle stranded RNA, approximately 18-23 nucleotides in length whichplays an important role in regulation of metabolic processes,particularly due to their involvement in regulation of stability andtranslation of mRNA encoding specific proteins. miRNA also participatein other important processes, like heterochromatin formation and genomerearrangement.

The terms “excessive” and “insufficient” in vivo cell death describe thesituation when the number of cells dying in a particular organ or tissueis respectively higher or lower than in age and gender matched controls.

As used herein, the terms “purified”, “decontaminated” and “sterilized”refer to the removal of contaminant(s) from a sample.

As used herein, the terms “substantially purified” and “substantiallyisolated” refer to nucleic acid sequences that are removed from theirnatural environment, isolated or separated, and are preferably 60% free,more preferably 75% free, and most preferably 90% free from othercomponents with which they are naturally associated. An “isolatedpolynucleotide” is therefore a substantially purified polynucleotide. Itis contemplated that to practice the methods of the present inventionpolynucleotides can be, but need not be substantially purified. Avariety of methods for the detection of nucleic acid sequences inunpurified form are known in the art.

As used herein, the terms “PCR product” and “amplification product”refer to the resultant mixture of compounds after two or more cycles ofthe PCR steps of denaturation, annealing and extension are complete.These terms encompass the case where there has been amplification of oneor more segments of one or more target sequences.

The term “urinary tract” as used herein refers to the organs and ductswhich participate in the secretion and elimination of urine from thebody.

“Patient” or “subject” as the terms are used herein, refer to therecipient of the treatment. Mammalian and non-mammalian patients areincluded. In a specific embodiment, the patient is a mammal, such as ahuman, canine, murine, feline, bovine, ovine, swine, or caprine. In aparticular embodiment, the patient is a human.

In one embodiment of the present invention, the detected miRNAsoriginate from and are specifically expressed in a specific cell type,tissue, or organ in the body, wherein alterations in the level of saidmiRNAs are indicative of acute pathology of said tissue, such as forexample acute myocardial infarction associated with death ofcardiomyocytes; brain stroke associated with death of neurons and glialcells; hepatitis or liver cirrhosis associated with hepatocyte deathcaused by a viral or other infection or by action of toxic agents; acutepancreatitis associated with death of different pancreatic cells;rejection of a transplanted organ associated with excessive cell deathin the transplanted organ; traumatic damage of various organs; numerousacute infections, for example tuberculosis associated with cell death inlungs and/or other infected organs.

In another embodiment of the present invention, the detected miRNAsoriginate from and are specifically expressed in a specific cell type,tissue, or organ in the body, wherein alterations in the level of saidmiRNAs are indicative of chronic pathology of said tissue, such as forexample Alzheimer's disease, Parkinson disease, frontotemporal dementiaand other diseases of the central nervous system that are caused oraccompanied by neuronal death; chronic heart failure associated with thedeath of cardiomyocytes, emphysema associated with death of lung cells;diabetes type 1 associated with the death of pancreatic beta cells,glomerulonephritis associated with the death of kidney cells,precancerous conditions associated with the apoptotic death of activelyproliferating precancerous cells, cancers associated with massivenecrotic cell death due to insufficient blood supply, and cell death inchronically infected organs or tissues.

In yet another embodiment of the present invention, the detected miRNAsoriginate from and are specifically expressed in a specific cell type,tissue, or organ in the body, and alterations in the level of saidmiRNAs are indicative of cytotoxic effects of physical and chemicalagents, such as for example radiation associated with relatively lowdoses that kill bone marrow cells higher doses that lead to the death ofepithelial cells of gastrointestinal system, and even higher doses thatkill brain neurons; and chemical cytotoxicity, associated with celldeath in different organ and tissues induced by natural or synthetictoxic compounds.

In yet another embodiment of the present invention, the detected miRNAsoriginate from and are specifically expressed in a specific cell type,tissue, or organ in the body and can be used for prognosis of diseaseoutcome. Changes in the levels of respective miRNAs, that are indicativeof disease progression/regression, success of therapeutic or surgicalintervention, are used for disease and treatment monitoring.

In another embodiment of the invention, the detected miRNAs originatefrom transplanted cells, tissues, or organs and their levels areindicative of rejection episodes and corresponding treatment.

In another embodiment of the invention, the detected miRNAs originatefrom a pathogen and are used for infection diagnosis and monitoring. Ina specific embodiment of the instant invention, the pathogen is a virus,for example Epstein-Barr virus.

In yet another embodiment of the invention, the detected miRNAsoriginate from cells of an infected organ and can be used for diagnosissupport, evaluation of infected tissue damage, and further disease andtreatment monitoring.

In yet another embodiment of the invention, the detected miRNAsoriginate from the fetus of a pregnant female, and are characteristic ofa condition or pathology of the fetus, such as for examplepre-eclampsia, which is characterized by excessive death of trophoblastsin placenta. In yet another embodiment, the detected miRNAs originatefrom a fetus of a pregnant female, and are characteristic of a conditionor pathology of the fetus, such as for example Down syndrome and othertrisomies accompanied by the delay of organ development and excessive orinhibited cell death.

In yet another embodiment of the invention, the information about thelevels of tissue or cell-specific miRNAs alone or in combination withother markers are used for diagnosis or monitoring of cancer andpre-cancerous conditions, such as for example liver cancer, kidneycancer, prostate cancer, colorectal cancer, pancreatic cancer and otherknown cancers.

In some embodiments, the levels of cell- and/or tissue-specific miRNAsare normalized using the levels of ubiquitous miRNA in serum, the levelsof albumin or creatinine in urine, or the levels of placenta-specificmiRNAs for normalization of other tissue-specific fetal miRNAs.

In one aspect of the invention, the step of analyzing said urine sampleto detect specific miRNAs includes a technique selected from the groupconsisting of hybridization, cycling probe reaction, polymerase chainreaction, nested polymerase chain reaction, PCR to analyze single strandconformation polymorphisms and ligase chain reaction.

In certain aspects of the invention, the nucleic acid degradation insaid urine sample is reduced. The method of reducing nucleic aciddegradation comprises inhibiting nuclease activity by use of RNAseinhibitors, or by treating said urine sample with a compound selectedfrom the group consisting of: guanidine-HCl, guanidine isothiocyanate,N-lauroylsarcosine, and sodium dodecylsulphate. In another aspect of theinvention, said urine sample has been held in the bladder less than 12hours.

In one embodiment of the present invention, the miRNA sequences measuredare specifically related to tissues in the body, which may be selectedfrom but are not limited to, lung, heart, liver, nervous system, brain,blood, kidney, bone, eye or pancreas.

The tissues selected for the analysis may be normal or abnormal (e.g.,malignant). Malignant tissues and tumors include carcinomas, sarcomas,melanomas and leukemia generally and more specifically selected frommalignant tissues and tumors associated with biliary tract cancer,bladder cell carcinoma, bone cancer, brain and CNS cancer, breastcancer, cervical cancer, choriocarcinoma, chronic myelogenous leukemia,colon cancer, connective tissue cancer, cutaneous T-cell leukemia,endometrial cancer, esophageal cancer, eye cancer, follicular lymphoma,gastric cancer, hairy cell leukemia, Hodgkin's lymphoma, intraepithelialneoplasms, larynx cancer, lymphomas, liver cancer, lung cancer (e.g.small cell and non-small cell), melanoma, multiple myeloma,neuroblastomas, oral cavity cancer, ovarian cancer, pancreatic cancer,prostate cancer, rectal cancer, renal cell carcinoma, sarcomas, skincancer, squamous cell carcinoma, testicular cancer, thyroid cancer, andrenal cancer. The method may be used to distinguish between benign andmalignant tumors.

Subjects from whom such tissue samples may be harvested include those atrisk of developing a cancer. A subject at risk of developing a cancer isone who has a high probability of developing cancer (e.g., a probabilitythat is greater than the probability within the general public). Thesesubjects include, for instance, subjects having a genetic abnormality,the presence of which has been demonstrated to have a correlativerelation to a likelihood of developing a cancer that is greater than thelikelihood for the general public, and subjects exposed to cancercausing agents (i.e., carcinogens) such as tobacco, asbestos, or otherchemical toxins, or a subject who has previously been treated for cancerand is in apparent remission.

The instant methods include isolation of miRNAs from the bodily fluidsof the patients. In one aspect of the invention, a miRNA of interest maybe detected in a body fluid such as blood, amniotic fluid, cerebrospinalfluid, plasma, milk, semen, serum, sputum, saliva and urine. In oneaspect of the instant invention, the miRNA is detected in urine. Inanother embodiment, the miRNA is detected in serum.

The instant method of the miRNA isolation of the instant invention canutilize commercially available anion exchange materials. Either strongor weak anion exchangers may be employed. By utilizing selectedsolutions for adsorption and elution, the miRNA can be purified,concentrated, and substantially isolated.

By employing a solution at known ionic strength for the initial bindingof the miRNA to the anion exchange column materials, most of the watersoluble components including other electronegative molecules such asproteins (weakly-bound contaminants) can be washed through the column.For elution, the required ionic strength is reached by using knownconcentrations of a salt such as NaCl, which may be mixed with a bufferto control pH, ideally corresponding to the lowest ionic strength atwhich the nucleic acids will completely elute. Contaminating substancesbound to the anion exchange resin with higher stringency than thenucleic acids may thereby be left within the column, i.e., strongerbound contaminants are separated away from the nucleic acids.

A preferred weak exchanger is one in which primary, secondary, ortertiary amine groups (i.e., protonatable amines) provide exchangesites. The strong base anion exchanger has quaternary ammonium groups(i.e., not protonatable and always positively charged) as exchangesites. Both exchangers are selected in relation to their respectiveabsorption and elution ionic strengths and/or pH for the miRNA beingseparated. The solution strengths are higher than the binding strengths.

In one aspect of the invention, a method is provided for isolationtranrenal miRNA from urine, the method comprising providing urine from asubject; optionally separating cells and cell debris from the urine byfiltration or centrifugation; adding EDTA and Tris-HCl to the urine,adding silica free anion exchange resin to urine, incubating themixture, removing the anion exchange medium from the urine, and elutingmiRNA from the resin.

In one embodiment of the method of isolating miRNA from urine, theconcentration of EDTA and Tris-HCl after it is added to the urine is ina range of 10-100 mM, and the pH of the solution is between about 8.0and about 8.5.

In a further embodiment, the body fluid is optionally pre-filteredthrough a membrane prior to adsorption onto the anion-exchange medium.

In a further embodiment, the anion exchange medium is a sepharose-basedresin functionalized with cationic quaternary ammonium groups. Examplesof sepharose-based resins, functionalized with cationic ammonium groupsinclude Q-Sepharose™ ANX-4 Sepharose™ Fast Flow, DEAE-Sepharose™, andQ-Sepharose-XL™ DEAE Sepharose Fast Flow (GE Healthcare).

In a further embodiment, the anion exchange medium is selected fromsepharose-based quaternary ammonium anion exchange medium such asQ-filters or Q-resin.

In a further embodiment of the invention, the anion-exchange medium isimmobilized on an individualized carrier wherein such a carrier is acolumn, cartridge or portable filtering system which can be used fortransport or storage of the medium/nucleoprotein bound complex.

In another embodiment of the present invention, periodic analysis ofmiRNA sequences present, for example, in the urine samples of the sameperson can give early information about a pathological process in aparticular organ or tissue. For example, miRNA122 is synthesized inliver only and increases in its amount may be a marker of hepatitis oranother liver pathology. Alzheimer's syndrome can be accompanied byincreases in the concentration of miRNA specifically expressed inneurons.

In another embodiment, more detailed monitoring of tissue-specific miRNAin the bodily fluid sample of the patient will be useful for estimationof a severity of the disease and for evaluation of effectiveness oftherapeutic efforts.

In yet another embodiment, in combination with analysis oftumor-specific mutations the data on the tissue-specific miRNA can helpin determination of tumor localization.

Other aspects of the instant invention relate to diseases caused by oraccompanied by changes in a specific miRNA(s) expression. The describedtechnology will help in diagnosis of such type pathologies.

In yet another embodiment, the application of the instant method may beextended to monitoring pharmacokinetics of synthetic siRNA in thepatient's urine to enhance optimization of the siRNA drug design.

Unless otherwise defined, all technical and scientific terms used hereinhave the same meaning as commonly understood by one of ordinary skill inthe art to which this invention pertains. Although methods and materialssimilar or equivalent to those described herein can be used in thepractice of the present invention, suitable methods and materials aredescribed below. All publications, patent applications, patents, andother references mentioned herein are expressly incorporated byreference in their entirety. In cases of conflict, the presentspecification, including definitions, will control. In addition, thematerials, methods, and examples described herein are illustrative onlyand are not intended to be limiting.

EXAMPLES

The examples are presented in order to more fully illustrate the variousembodiments of the invention. These examples should in no way beconstrued as limiting the scope of the invention recited in the appendedclaims.

Example 1 Extraction of miRNA from Urine

Urine Collection:

For these experiments, urine specimens from patients or volunteers werecollected in a sterile 110 ml urine collection cup and were immediatelysupplemented with EDTA up to final concentration between 10 and 150 mM,preferably 50 mM. Specimens were stored in 10-50 ml aliquots at −80° C.Optional filtration of urine was carried out on Stericup™ (Millipore,Vacuum Driven Filtration System, 0.45μ Durapore™ filter) immediatelyafter specimen collection before the EDTA was added.

Q Binding:

In a 50 ml tube 20 mL of urine was diluted with equal volume of 50 mMEDTA (pH 8.0) and 50 mM Tris-HCl (pH 8.0) which was then supplementedwith 1-2 ml of Q-Sepharose™ (GE Healthcare; 17-0510-10) slurry andrigorously mixed 10-30 min at room temperature. The resin, with boundnucleic acids, was collected by centrifugation at 2000 g for 5 minutesat room temperature in a table top clinical centrifuge using a swingbucket rotor. All but 500 μl of supernatant was removed by aspiration.The resin pellet was resuspended in the remaining supernatant andtransferred to a Micro Bio-Spin Chromatography Column (Bio-Rad) orequivalent, which was operated either by centrifugation of vacuum. Theresin in the column was washed three times with 500 μl 2×SSC (300 mMNaCL/30 mM sodium citrate (pH 7.0)) or with buffer with comparable ionicstrength (e.g. 300 mM NaCl or LiCl). Nucleic acids can be eluted fromQ-Sepharose with high ionic strength (e.g. 1M NaCl or LiCl) but themethods described below preserves RNA better.

Elution from Q-Sepharose™ and TRIzolTm Phase Separation:

Bound nucleic acids were further eluted with 500 μl of TRIzolTm reagent(Invitrogen). The extraction of nucleic acids from TRIzol was carriedout according manufacturer's recommendations. Briefly, for phaseseparation TRIzol eluate was supplemented with 100 μl chloroform, mixedvigorously, incubated at room temperature for 3-5 minutes andcentrifuged at 12,000×g for 15 min at 4° C. While avoiding touching theinterphase, 300 μl of the upper phase was transferred into a freshcentrifuge tube. Then the nucleic acids were precipitated oradditionally cleaned and desalted on a silica column.

Nucleic Acid Precipitation:

For nucleic acid precipitation, the above described preparation wassupplemented with 1 μl of 20 mg/mL glycogen (Roche) and 300 μl of 100%isopropyl alcohol. Nucleic acids were collected by centrifugation, thepellet was washed twice with 200 μl of 70% ethanol, allowed to air dryfor 5 min at room temperature, and then the nucleic acids were dissolvedin 30 μl of 0.1 mM EDTA/1×RNA Secure (Ambion). The samples wereincubated at 60° C. for 10 min to inactivate any residual RNaseactivity.

Silica Column Cleaning of Nucleic Acids:

For binding to a silica column (Qiagen PCR clean columns or equivalent)3 volumes of 96% ethanol were added to nucleic acid preparation from theTRIzol upper phase, and, after 3 minutes incubation at room temperature,the mixture was loaded onto the column. The column was washed twice with500 μl 2 M LiCl/80% ethanol and twice with 500 μl 80% ethanol. Nucleicacids were eluted with 50 μl of 0.1 mM EDTA/1×RNA Secure (Ambion). Thesamples were incubated at 60° C. for 10 min to inactivate any residualRNase.

DNase I and RNase A Digestion:

To verify the nucleic acid identity of the material extracted from urinewith the above described protocol, the instant prep was digested withDNase I and/or RNase A. DNase I digestion was carried out in the DNase IReaction Buffer (NEB) containing 2 units of RNase free DNase I (NEB).RNase A digestion was performed in TE buffer supplemented with 50 ng/mLboiled RNase A. Samples were incubated at 37° C. for 60 min and afteraddition of loading dye samples were subjected to electrophoresis on 5%polyacrylamide 1×TBE gels and stained with 1/10000 diluted SYBR® Gold(Invitrogen). As shown in FIG. 1, the isolated material represents lowmolecular weight nucleic acids, mainly RNA and their fragments. Inaddition, (see FIG. 1), for comparison nucleic acids from Q-resin wereeluted by 3 M NaCl, lanes 2 and 3, and Trizol™, lanes 4 and 5.

In the FIG. 1, lanes 1 and 5, represent nucleic acids isolated with highsalt and TriZol elution from Q-Sepharose, respectively; lanes 2 and 6; 3and 7; 4 and 8, represent nucleic acids after treatment with DNAse,RNAse, or DNAse plus RNAse, respectively.

Also, to demonstrate existence and molecular size of RNA, RNA aliquotsof purified nucleic acids were digested with DNaseI, lanes 3 and 5.

Extraction of RNA from Serum

For these experiments, 1.2 ml of TRIzol LS were added to 0.4 ml ofserum, and the mixture was centrifuged 10 at 14,000 rpm. The supernatantwas transferred into a 2 ml Eppendorf tube, 0.3 ml of chloroform wasadded, and the mixture was shaken for 15 seconds. After centrifugationat 14,000 rpm for 15 min, the supernatant was transferred into a 5 mltube and ethanol was added up to final concentration of 70%. The mixturewas loaded on a Quiagen Quick column on a vacuum manifold, and thecolumn was washed twice with 0.5 ml of 2M LiCl-80% EtOH, once with 0.5ml of 80% ethanol-80 mM sodium acetate (pH 5.0), and finally with 0.5 mlof 95% ethanol. The column was centrifuged in 1.5 ml Eppendorf tube 3min at 14,000 rpm, and RNA was eluted with 40 μl H₂O.

Example 2

This Example demonstrates that miRNA, from dying cells, cross the kidneybarrier and may be detected in the urine of a patient.

Detection of Human miRNA Molecules in Urine

Micro RNA species that were analyzed in this example can be grouped inthree distinct types, namely ubiquitous miRNAs, which are expressed inall or multiple tissues, tissue-specific miRNAs, and miRNAs in whichexpression is significantly altered in a particular tissue or cell type.As shown by Table 1, 20 different miRNAs were obtained from urine of 16healthy volunteers and enrolled donors and later detected by real timeRT-PCR using commercially available miRNA expression analysis kit (ABI).Corresponding synthetic miRNA oligonucleotides were used as standards.Reactions were carried out strictly as recommended by the supplier.

TABLE 1 Detected miRNA SEQ ID NO: ID Sequence Expression 1 hsa-miR-127UCGGAUCCGUCUGAGCUUGGCU Brain overexpressed 2 hsa-miR-153UUGCAUAGUCACAAAAGUGA Brain overexpressed 3 hsa-miR-129CUUUUUGCGGUCUGGGCUUGC Brain-specific 4 hsa-miR-137UAUUGCUUAAGAAUACGCGUAG Brain overexpressed 5 hsa-miR-218UUGUGCUUGAUCUAACCAUGU Ubiquitous, Brain overexpressed 6 hsa-miR-219UGAUUGUCCAAACGCAAUUCU Brain-specific 7 hsa-miR-128aUCACAGUGAACCGGUCUCUUUU Brain-specific 8 hsa-miR-9UCUUUGGUUAUCUAGCUGUAUGA Brain overexpressed 9 hsa-miR-138AGCUGGUGUUGUGAAUC Brain, Thyroid 10 hsa-miR-134 UGUGACUGGUUGACCAGAGGGBrain and several other tissues 11 hsa-miR-124a UUAAGGCACGCGGUGAAUGCCABrain-specific 12 hsa-miR-122a UGGAGUGUGACAAUGGUGUUUGU Liver-specific 13hsa-miR-133a UUGGUCCCCUUCAACCAGCUGU Heart and Muscle overexpressed 14hsa-miR-1 UGGAAUGUAAAGAAGUAUGUA Heart and Muscle overexpressed 15hsa-miR-335 UCAAGAGCAAUAACGAAAAAUGU Ubiquitous 16 hsa-miR-16UAGCAGCACGUAAAUAUUGGCG Ubiquitous 17 hsa-miR-215 AUGACCUAUGAAUUGACAGACSmall intestine and colon overexpressed 18 hsa-miR-135bUAUGGCUUUUCAUUCCUAUGUG Placenta-overexpressed 19 hsa-miR-517cAUCGUGCAUCCUUUUAGAGUGU Placenta-overexpressed 20 hsa-miR-518eAAAGCGCUUCCCUUCAGAGUGU Placenta-overexpressed

All three types of miRNA were detected in most preps of urinary RNA. Thehighest copy numbers were characteristic of ubiquitous miRNA. However,tissue-specific miRNA or miRNA over-expressed in a particular tissue orcell type were also detectable. It has been unequivocally demonstratedthat a portion of miRNA from dying cells is not degraded but appears inthe bloodstream and is finally excreted into urine.

Example 3

The Example demonstrates that miRNA from human nasopharyngeal carcinoma(NPC) cells can cross the patient's kidney barrier and can be detectedin patient's urine by real time RT-PCR.

Virus-Derived miRNA in Urine

It is known that some viruses also encode and produce miRNAs. SinceEpstein-Barr virus (EBV) is involved in development of nasopharyngealcarcinoma (NPC), the instant system was used to find out if viral miRNAfrom NPC cells can reach a patient's urine and be detected there. Urinesamples from NPC patients were collected and stored according to theprocedures described in the Example 1 of this application. EBV infectionwas confirmed by the detection of virus-specific DNA sequences in urine.Urine collected from healthy donor was negative for EBV specific DNAsequences. Two EBV-specific miRNAs BART3-3p and BART1-3p were analyzedin this study:

SEQ ID NO: 21 BART3-3P CGC ACC ACU AGU CAC CAG GUG U SEQ ID NO: 22BART1-3P UAG CAC CGC UAU CCA CUA UGU CU

Reverse transcription was performed in 15 μl, one tenth of the RTreaction was subjected to PCR amplification using JumpStart DNApolymerase from Sigma. The following primers were used at 500 nMconcentration:

SEQ ID ID Sequence NO: BART3-3PRT GTC GTA TCC AGT GCA GGG TCC GAG GTA 23TTC GCA CTG GAT ACG ACA CAC CT BART1-3PRTGTC GTA TCC AGT GCA GGG TCC GAG GTA 24 TTC GCA CTG GAT ACG ACA GAC ATBART3-3PF CGC CGC ACC ACT AGT CAC 25 BART1-3PF CGC TAG CAC CGC TAT CCA26 miRNACR GTG CAG GGT CCG AGG T 27

Products were analyzed in 15% polyacrylamide gel (PAAG).

As demonstrated by FIG. 2, both BART3 and BART 1 miRNA species weredetected in urine from NPC patients but not in the urine sample from ahealthy donor. These data again indicate that miRNA from dying cellslocated outside of urinary system can be detected in the urine. In theFIG. 2, lane 1, represents markers; lanes 2 and 3, represent patientswith nasopharyngeal carcinoma, lanes 4 and 5, represent controlpatients, and lane 6, represents positive control, which representsrespective synthetic miRNAs.

Example 4

This example demonstrates that the neuronal death caused by stroke canbe registered in vivo by measurements of the concentrations ofneuron-specific miRNA in the patient's urine.

Brain Stroke Diagnosis

For these experiments, patients with brain stroke were investigated foranalysis of changes in concentrations of brain-specific miRNA or miRNAwhich are over-expressed in brain, after stroke. Since currently it isnot known in what brain cell types and in what brain areas these miRNAare expressed, 9 different brain specific miRNA were studied.

Patients:

Urine samples were collected from patients accepted at a hospitalthrough the emergency room. Diagnosis of brain stroke was based onclinical symptoms. Urine samples were collected at 12 and 24 hours afterthe stroke. Control urine samples were donated by age matched volunteersbut without stroke symptoms. Samples were collected and stored accordingto the procedures described in the Example 1 of this application.

miRNA Species:

miRNA from urine was extracted according to the procedure described inthe Example 1. An amount of RNA equivalent to that isolated from 675 μlof urine underwent reverse transcription PCR and 1/10 of the RT-PCRmixture underwent final real time PCR, which was carried out using theprotocol provided by the manufacturer. Data obtained were normalized forindividual kidney filtration rates by re-calculation per creatinineconcentration in urine. For these experiments, urine samples collectedfrom healthy donors from same age group were used as baseline. DifferentmiRNA species are presented as follows:

A. hsa-mir-128a B. hsa-mir-9 C. hsa-mir-127 D. hsa-mir-137 E.hsa-mir-129 F. hsa-mir-219 G. hsa-mir-218

Results summarized in FIGS. 3A to 3G clearly demonstrate that afterbrain stroke, there is a significant increase in the levels of severalbrain specific miRNA (128a, 129, 218, 219)—reflecting kinetics of thebrain cell death.

Example 5

This example demonstrates that kinetics of the miRNA concentrations inpatient's urine after stroke provides information about disease outcome.

Brain Stroke Monitoring

For the experiments, patients with brain stroke were investigated foranalysis of correlation between changes in concentrations ofbrain-specific miRNA and disease development.

Patients:

Urine samples were collected from patients accepted at a hospitalthrough the emergency room. Diagnosis of brain stroke was based onclinical symptoms and MRI analysis. Urine samples were collected at 12,24, 48 hours and a week after the stroke. Patient clinical status wasevaluated 30 days after stroke. Control urine samples were donated byage matched volunteers but without stroke symptoms. Samples werecollected and stored according to the procedures described in theExample 1 of this application.

miRNA Species:

miRNA from urine was extracted according to the procedure described inExample 1 and analyzed with TaqMan miRNA assays (Applied Biosystems). Anamount of RNA equivalent to that isolated from 400 μl of urine underwentreverse transcription PCR and 1/10 of the RT-PCR mixture underwent finalreal time PCR, which was carried out using the protocol provided by themanufacturer. Data obtained were normalized for individual kidneyfiltration rates by re-calculation per creatinine concentration inurine. For these experiments, urine samples collected from healthydonors from same age group were used as baseline.

Results summarized in FIGS. 4A and B clearly demonstrate that thedynamics of changes in Tr-miRNA 129 and Tr-miRNA 219 after brain strokeare different in different patients and correlates with the diseasedevelopment. The increase in neuronal death a week after stroke inpatient #3 corresponds to worsening in the patient clinical status. Atthe same time two patients, whose transrenal neuron-specific miRNA hadtendency to normalization, demonstrated significant improvement.

Example 6 Alzheimer's Disease Diagnosis

Alzheimer's disease is a progressive neurological disease that is causedby the death of neurons, particularly in the cortex and hippocampus. Thediagnosis is based on neurological examination and the exclusion ofother causes of dementia whereas the definitive diagnosis can be madeonly at autopsy. The instant invention demonstrates that excessiveneuronal death characterizing Alzheimer's disease may be monitored bymeasuring levels of specific brain miRNAs isolated from the patient'surine.

For these experiments, patients diagnosed with Alzheimer's disease wereinvestigated for analysis of changes in concentrations of brain-specificor over-expressed miRNA as a result of neuronal death.

Patients:

Urine and serum samples were collected from patients diagnosed withvarious stages of the Alzheimer's disease. Control urine and serumsamples were donated by age matched volunteers but without symptoms ofAlzheimer's disease. Samples were collected and stored according to theprocedures described in the Example 1 of this application. Some urinesamples were filtered after collection as described in Example 1 todelete cells and cell debris.

miRNA Species:

RNA from urine and serum was extracted according to the proceduresdescribed in the Example 1.

In one set of experiments an amount of RNA equivalent to that isolatedfrom 750 μl of urine underwent reverse transcription PCR and 1/10 of theRT-PCR mixture underwent final real time PCR, which was carried outusing the protocol provided by the manufacturer (Applied Biosystems).Data obtained were normalized for individual kidney filtration rates byre-calculation per creatinine concentration in urine. FIG. 5 clearlydemonstrates that concentrations of several brain specific miRNAs isincreased in the urine of Alzheimer's patients.

In another set of experiments, RNA isolated from filtered urine or serumwas analyzed. An amount of RNA equivalent to that isolated from 0.6 mlof urine or 50 μl of serum underwent reverse transcription PCR and 1/10of the RT-PCR mixture underwent final real time PCR, which was carriedout using the protocol provided by the manufacturer (AppliedBiosystems). Data obtained for urinary miRNA were normalized forindividual kidney filtration rates by re-calculation per creatinineconcentration in urine. Data obtained for plasma miRNA were normalizedper ubiquitous miRNA-16. FIGS. 6 and 7 show that the levels of someneuron-specific miRNAs are higher in both filtered urine and serum ofthe Alzheimer's patients compared to age-matched controls.

Example 7 Parkinson's Disease

Parkinson's disease is a degenerative disorder of the central nervoussystem that often impairs the sufferer's motor skills and speech. Theinstant invention demonstrates that excessive cellular death ofdopaminergic neurons, characterizing Parkinson's disease may bemonitored by measuring levels of specific brain miRNAs isolated from thepatient's urine.

For these experiments, patients diagnosed with Parkinson's wereinvestigated for analysis of changes in concentrations of brain-specificmiRNA or over-expressed miRNA as a result of neuronal death.

Patients:

Urine samples were collected from patients diagnosed with various stagesof the Parkinson's disease. Control urine samples were donated by agematched volunteers without symptoms of Parkinson's disease. Samples werecollected and stored according to the procedures described in theExample 1 of this application.

miRNA Species:

For these experiments, RNA from urine was extracted according to theprocedure described in the Example 1. Amount of RNA equivalent to thatisolated from 750 μl of urine underwent reverse transcription PCR and1/10 of the RT-PCR mixture underwent final real time PCR, which wascarried out using the protocol provided by the manufacturer (AppliedBiosystems). Data obtained were normalized for individual kidneyfiltration rates by re-calculation per creatinine concentration inurine. FIG. 8 demonstrates that concentrations of several brain specificmiRNAs is increased in the urine of the patients with Parkinson disease.

Example 8 Prenatal Testing for Pregnancy-Related or Fetal Diseases

The principal finding of permeability of the kidney barrier for miRNAmolecules opens the way for the use of maternal urine to performcompletely noninvasive prenatal diagnosis of congenital diseases. Onecan perform such a noninvasive screen as follows.

First, a sample of urine is gathered from a pregnant patient. Wheredesired, miRNA in the urine sample is then be isolated, purified and/ortreated to prevent degradation using methods described above. MiRNAprofiling is then performed using quantitative PCR or miRNA array andthe data obtained are used to determine different fetal pathologies, asdescribed for other pathologies above.

Example 9 Down Syndrome

For the experiments, differences in concentrations of brain-specificmiRNA in maternal urine between women pregnant with normal and Downsyndrome fetuses were investigated.

Patients:

Urine samples were collected from pregnant women diagnosed with Downsyndrome by amniocentesis. Control urine samples were donated by agematched women with normal pregnancies. Samples were collected and storedaccording to the procedures described in the Example 1 of thisapplication.

miRNA Species:

miRNA from urine was extracted according to the procedure described inthe Example 1. An amount of RNA equivalent to that isolated from 750 μlof urine underwent reverse transcription PCR and 1/10 of the RT-PCRmixture underwent final real time PCR, which was carried out using theprotocol provided by the manufacturer. Data obtained were normalized perplacenta-specific miRNA 518. FIG. 9 demonstrates lower concentration thebrain-specific miRNA 9 in urine of women pregnant with Down syndromefetuses compared to urine of women with normal pregnancies, whichindicates insufficient cell death compared to respective controls.

1. A method of detecting at least one cell-free miRNA released from at least one cell in a subject, the method comprising: a) separating a soluble fraction of a sample of urine or blood obtained from a subject; and b) detecting and quantitating at least one cell-free miRNA in the soluble fraction with at least one oligonucleotide primer or probe that is substantially complementary to a part of said at least one cell-free miRNA, wherein the at least one cell-free miRNA is indicative of in vivo cell death associated with a disease or disorder.
 2. The method of claim 1, wherein said disorder is a brain stroke.
 3. The method of claim 1, wherein said disorder is Alzheimer's disease.
 4. The method of claim 1, wherein said disorder is Parkinson's disease.
 5. The method of claim 1, wherein said at least one cell-free miRNA is associated with fetal pathology.
 6. The method of claim 5, wherein said fetal pathology is Down syndrome.
 7. The method of claim 1, wherein said disorder is a pathogen infection, such as a virus infection.
 8. The method of claim 1, wherein said detecting and quantitating diagnoses said disease or disorder.
 9. The method of claim 1, wherein said detecting and quantitating is repeated over time to monitor the progression or regression of said disease or disorder.
 10. A method of detecting at least one cell-free miRNA released from at least one cell in a subject, the method comprising: a) separating a soluble fraction of a sample of urine or blood obtained from a subject; and b) detecting and quantitating at least one cell-free miRNA in the soluble fraction with at least one oligonucleotide primer or probe that is substantially complementary to a part of said at least one cell-free miRNA, wherein the at least one cell-free miRNA is indicative of in vivo cell death associated with acute pathology, chronic pathology, or the cytotoxic effect of physical or chemical agents.
 11. The method of claim 10, wherein the acute pathology is selected from acute myocardial infarction associated with death of cardiomyocytes, hepatitis or liver cirrhosis associated with hepatocyte death caused by a viral or other infection or by action of toxic agents, acute pancreatitis associated with death of different pancreatic cells, rejection of a transplanted organ associated with excessive cell death in the transplanted organ, traumatic damage of various organs, acute infections, or tuberculosis associated with cell death in lungs and/or other infected organs.
 12. The method of claim 10, wherein the chronic pathology is selected from frontotemporal dementia, chronic heart failure associated with the death of cardiomyocytes, emphysema associated with death of lung cells, diabetes type 1 associated with the death of pancreatic beta cells, glomerulonephritis associated with the death of kidney cells, precancerous conditions associated with the apoptotic death of actively proliferating precancerous cells, cancers associated with massive necrotic cell death due to insufficient blood supply, and cell death in chronically infected organs or tissues.
 13. The method of claim 10, wherein the cytotoxic effect of physical or chemical agents is selected from radiation associated with doses that kill bone marrow cells, doses that lead to the death of epithelial cells of gastrointestinal system, and doses that kill brain neurons, and chemical cytotoxicity associated with cell death in different organ and tissues induced by natural or synthetic toxic compounds.
 14. A method of determining the prognosis the outcome of a disease or disorder, the method comprising: a) separating a soluble fraction of a sample of urine or blood obtained from a subject; and b) detecting and quantitating at least one cell-free miRNA in the soluble fraction with at least one oligonucleotide primer or probe that is substantially complementary to a part of said at least one cell-free miRNA, wherein the at least one cell-free miRNA is indicative of the outcome of a disease or disorder.
 15. The method of claim 14, wherein a change in the level of the at least one cell-free miRNA over time is indicative of the progression or regression of a disease or disorder, or is indicative of the success of therapeutic or surgical intervention, or monitors progress of a treatment in the subject.
 16. The method of claim 1, wherein said sample is urine.
 17. The method of claim 1, wherein said soluble fraction is serum.
 18. The method of claim 1, wherein said soluble fraction is plasma. 